After having defected to the West, a Soviet scientist has developed a new weapon that would change the world, the Shagohod missile system, but he was sent back as part of a deal within the Cuban Missile Crisis. Now the West wants him back, and Naked Snake goes to rescue him. However, legendary soldier The Boss, defects to the USSR., and the Soviet colonel that she now serves explodes a nuclear weapon against his own countrymen. The Soviet leaders blame the U.S. for the nuclear attack and threaten retaliation unless the U.S. can prove its innocence in the matter. A deal is made between the East and West: the U.S. must assassinate The Boss and her Cobra Squad, eliminate the Soviet colonel, rescue the scientist once again and destroy the prototype Shagohod within one week or risk a nuclear war with the Soviet Union. Seen as being responsible for letting The Boss get away, Snake must complete the mission or he will be executed.